Michael McKenna (MCKMICP at YaleVM.YCC.Yale.Edu) wrote:
> I would like to generate a phylogenetic tree of the lipocalin
> superfamily. These sequences are very distantly related, if at
> all, but share a number of common general characteristics, including
> a signal peptide, several pairs of cysteine residues, and a
> molecular weight between 15 and 20 kD. They also share a common
> function; the transport and delivery of hydrophobic molecules
> through an aqueous environment. Several of these molecules have
> had their structures solved, and there is a compelling uniformity
> to their structure, even though the identity is very low at the
> primary level, often on the order of 20%.
>> I have discovered a number of potential lipocalins in the antennae of
> Drosophila melanogaster which belong to the family of odorant-binding
> proteins. My question is- Is it possible to generate a phylogeny from
> sequence data when only dubious connections can be made with various
> allignment algorithms. Most of the programs I have seen can do a
> resonable job with clearly related molecules. I suspect it can't
> be done reasonably in this particular case. Any suggestions?
> Thanks, Mike McKenna MCKMICP at YALEVM.YCC.Yale.edu
Michael McKenna,
With regard to your query about a phelogeny of lipocalins,
I have actually produced such a tree as part of a course
assignment here at UCSD. My phylogeny had 17 members, and I
feel confident that it is genuine. The results showed
reasonable clustering of similar proteins such as retinol
binding proteins, lactoglobulins, and insecticyanins. The
tree was made with a program called TREE as described by
Feng and Doolittle in Methods in Enzymology volume 183,
pages 375 - 387. Though the proteins I included have amino
acid sequences which are distantly related and often fall
within 20 - 25% identity, careful comparisons by randomizing
the questionable proteins' sequences eliminated doubt about
validity as members of the lipocalin family. If you would
like a copy of my tree and alignment, I would be happy to
mail it to you. I am currently working on a senior research
project trying to expand my tree. The work is being conducted
in the laboratory of R. Doolittle.
Carol Healey UCSD
ch at zeus.ucsd.edu